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The importance of segmental duplications and copy number variants as a source of genetic and phenotypic variation is gaining greater appreciation, in a variety of organisms. Now, we have identified the  Phytophthora sojae  avirulence genes  Avr1a  and  Avr3a  and demonstrate how each of these  Avr  genes display copy number variation in different strains of  P. sojae . The  Avr1a  locus is a tandem array of four near-identical copies of a 5.2 kb DNA segment. Two copies encoding  Avr1a  are deleted in some  P. sojae  strains, causing changes in virulence. In other  P. sojae  strains, differences in transcription of  Avr1a  result in gain of virulence. For  Avr3a , there are four copies or one copy of this gene, depending on the  P. sojae  strain. In  P. sojae  strains with multiple copies of  Avr3a , this gene occurs within a 10.8 kb segmental duplication that includes four other genes. Transcriptional differences of the  Avr3a  gene among  P. sojae  strains cause changes in virulence. To determine the extent of duplication within the superfamily of secreted proteins that includes Avr1a and Avr3a, predicted RXLR effector genes from the  P. sojae  and the  P. ramorum  genomes were compared by counting trace file matches from whole genome shotgun sequences. The results indicate that multiple, near-identical copies of RXLR effector genes are prevalent in oomycete genomes. We propose that multiple copies of particular RXLR effectors may contribute to pathogen fitness. However, recognition of these effectors by plant immune systems results in selection for pathogen strains with deleted or transcriptionally silenced gene copies.

Copy Number Variation and Transcriptional Polymorphisms of Phytophthora sojae RXLR Effector Genes Avr1a and Avr3a